Pierre Nicolas

Contact information

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Tel: +33-(0)1 3465 2894

Mailing address:
Unité MaIAGE. Bât 233
INRA - Domaine de Vivert
F-78350 Jouy-en-Josas, France

I work as a researcher at the INRA Jouy-en-Josas campus in the MaIAGE laboratory ("Mathématiques et Informatique Appliquées du Génome à l'Environnement"). My research focuses mainly on statistical bioinformatics with applications to bacterial genome analysis (genome analysis, transcriptomics, population genetics).

Some links

  • The Statistique et Génome laboratory (CNRS-INRA-Université d'Evry) where I prepared my PhD in Biomathematics (2003).
  • The Computational Biology Department at University of Southern California where I was a postdoc (2004-2005).
  • The SSB research group in statistics for biology.
  • The StatInfOmics team in MaIAGE
  • Basysbio, a former European project in which I was involved.
  • SHOW, a powerful self-training bacterial gene detection program (among other things) that I developped during my PhD.
  • TREEMM, a program that I developped for de novo identification of Sigma factor binding sites based on promoter sequence and expression data.
  • A page in memory of Philippe Bessières.
  • A laser-cut peristaltic pump that we designed to operate miniature bioreactors such as used in experimental evolution.
  • Mémoire d'Habilitation à Diriger des Recherche (HDR, in French)
  • Data browsers for large transcriptomics data sets on Bacillus subtilis and Staphylococcus aureus.


  • B.-H. Lee, D. Garmyn, L. Gal, C. Guérin, L. Guillier, A. Rico, B. Rotter, P. Nicolas, P. Piveteau (2019) Exploring Listeria monocytogenes transcriptomes in correlation with divergence of lineages and virulence as measured in Galleria mellonella. Appl Environ Microbiol. Epub ahead of print. (PubMed). (DOI: 10.1128/AEM.01370-19)

  • K. Sundell, L. Landor, P. Nicolas, J. Jørgensen, D. Castillo, M. Middelboe, I. Dalsgaard, V. Donati, L. Madsen and T. Wiklund (2019) Phenotypic and genetic predictors of pathogenicity and virulence in Flavobacterium psychrophilum. Front. Microb. 10 (PubMed). (DOI: 10.3389/fmicb.2019.01711).

  • C. Knupp, G.D. Wiens, M. Faisal, D.R. Call, K.D. Cain, P. Nicolas, D. Van Vliet, C. Yamashita, J.A. Ferguson, D. Meuninck, H.M. Hsu, D.B. Baker, L. Shen, T.P. Loch (2019) Large-scale Analysis of Flavobacterium psychrophilum MLST Genotypes Recovered From North American Salmonids Indicates Both Newly Identified and Recurrent Clonal Complexes are Associated with Disease. Appl Environ Microbiol. 85. pii: e02305-18. (PubMed). (DOI: 10.1128/AEM.02305-18).

  • E. Duchaud, T. Rochat, C. Habib, P. Barbier, V. Loux, C. Guérin, I. Dalsgaard, L. Madsen, H. Nilsen, K. Sundell, T. Wiklund, N. Strepparava, T. Wahli, G. Caburlotto, A. Manfrin, G.D. Wiens, E. Fujiwara-Nagata, R. Avendaño-Herrera, J.-F. Bernardet, P. Nicolas (2018). Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum. Front. Microb. 9 138. (PubMed). (DOI: 10.3389/fmicb.2018.00138).

  • T. Rochat, E. Fujiwara-Nagata, S. Calvez, I. Dalsgaard, L. Madsen, A. Calteau, A. Lunazzi, P. Nicolas, T. Wiklund, J.-F. Bernardet, E. Duchaud (2017) Genomic characterization of Flavobacterium psychrophilum serotypes and development of a multiplex PCR-based serotyping scheme. Front. Microbiol. 8. 1752. (PubMed). (DOI: 10.3389/fmicb.2017.01752).

  • G. Huet des Aunay, M. Grenna, H. Slabbekoorn, P. Nicolas, L. Nagle, G. Leboucher, G. Malacarne, T.I. Draganoiu. (2017) Negative impact of urban noise on sexual receptivity and clutch size in female domestic canaries. Ethology. 123. 843-853. (DOI: 10.1111/eth.12659)

  • V. Bidnenko, P. Nicolas, A. Grylak-Mielnicka, O. Delumeau, S. Auger, A. Aucouturier, C. Guérin, F. Repoila, J. Bardowski, S. Aymerich, E. Bidnenko (2017) Termination factor Rho: From the control of pervasive transcription to cell fate determination in Bacillus subtilis. PLoS Genet. 13. e1006909. (PubMed). (DOI: 10.1371/journal.pgen.1006909).

  • S.-M. Deutsch, M. Mariadassou, P. Nicolas, S. Parayre, R. Le Guellec, V. Chuat, V. Peton, C. Le Maréchal, J. Burati, V. Loux, V. Briard-Bion, J. Jardin, C. Plé, B. Foligné, G. Jan, H. Falentin (2017) Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study. Sci Rep. 7. 46409. (PubMed). (DOI: 10.1038/srep46409).

  • T. Rochat, P. Barbier, P. Nicolas, V. Loux, D. Pérez-Pascual, J.A. Guijarro, J.-F. Bernardet, and E. Duchaud. (2017) Complete Genome Sequence of Flavobacterium psychrophilum Strain OSU THCO2-90, Used for Functional Genetic Analysis. Genome Announc. 5. e01665-16. (PubMed). (DOI: 10.1128/genomeA.01665-16).

  • M.-H. Guinebretière, V. Loux, V. Martin, P. Nicolas, V. Sanchis, and V. Broussolle. (2017) Draft Genome Sequences of 18 Psychrotolerant and 2 Thermotolerant Strains Representative of Particular Ecotypes in the Bacillus cereus Group. Genome Announc. 5. e01568-16. (PubMed). (DOI: 10.1128/genomeA.01568-16).

  • D.R. Reuß, J. Altenbuchner, U. Mäder, H. Rath, T. Ischebeck, P.K. Sappa, A. Thürmer, C. Guérin, P. Nicolas, L. Steil, B. Zhu, T. Feussner, S. Klumpp, R. Daniel, F.M. Commichau, U. Völker, J. Stülke (2017) Large-scale reduction of the Bacillus subtilis genome: Consequences for the transcriptional network, resource allocation, and metabolism. Genome Res. 27. 289-299 (PubMed). (DOI: 10.1101/gr.215293.116).

  • R.A. Mars, P. Nicolas, E.L. Denham, and J.M. van Dijl. (2016) Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression. Microbiol Mol Biol Rev. 80. 1029-1057. (PubMed). (DOI: 10.1128/MMBR.00026-16).

  • T. Eychenne, E. Novikova, M.B. Barrault, O. Alibert, C. Boschiero, N. Peixeiro, D. Cornu, V. Redeker, L. Kuras, P. Nicolas, M. Werner, and J. Soutourina (2016) Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture. Genes Dev. 30. 2119-2132. (PubMed). (DOI: 10.1101/gad.285775.116).

  • U. Mäder, P. Nicolas, M. Depke, J. Pané-Farré, M. Debarbouille, M. van der Kooi-Pol, C. Guérin, S. Dérozier, A. Hiron, H. Jarmer, A. Leduc, S. Michalik, E. Reilman, M. Schaffer, F. Schmidt, P. Bessières, P. Noirot, M. Hecker, T. Msadek, U. Völker, and J.M. van Dijl (2016). Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions. PLoS Genet. 12. e1005962. (PubMed). (DOI: 10.1371/journal.pgen.1005962).

  • D. Van Vliet, G.D. Wiens, T.P. Loch, P. Nicolas, and M. Faisal. (2016) Genetic diversity of Flavobacterium psychrophilum isolated from three Oncorhynchus spp. in the U.S.A. revealed by multilocus sequence typing. Appl Environ Microbiol. 82. 3246-55. (PubMed). (DOI: 10.1128/AEM.00411-16).

  • S. McGovern, S. Baconnais, P. Roblin, P. Nicolas, P. Drevet, H. Simonson, O. Piétrement, J.-B. Charbonnier, E. Le Cam, P. Noirot, and F. Lecointe (2016) C-terminal region of bacterial Ku controls DNA bridging, DNA threading and recruitment of DNA ligase D for double strand breaks repair. Nucleic Acids Res. 44. 4785-4806. (PubMed). (DOI: 10.1093/nar/gkw149).

  • R. Avendaño-Herrera, R. Irgang, C. Sandoval, P. Moreno-Lira, A. Houel, E. Duchaud, M. Poblete-Morales, P. Nicolas, and P. Ilardi (2016) Isolation, Characterization and Virulence Potential of Tenacibaculum dicentrarchi in Salmonid Cultures in Chile. Transbound Emerg Dis. 63. 121-6. (PubMed). (DOI: 10.1111/tbed.12464).

  • T. Lacroix, S. Thérond, M. Rugeri, P. Nicolas, A. Gendrault, V. Loux, and J.-F. Gibrat (2016). Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT. Bioinformatics. 32. 1083-4. (PubMed). (DOI: 10.1093/bioinformatics/btv689).

  • R.A. Mars, P. Nicolas, M. Ciccolini, E. Reilman, A. Reder, M. Schaffer M, U. Mäder, U. Völker U, J.M. van Dijl, and E.L. Denham (2015). Small Regulatory RNA-Induced Growth Rate Heterogeneity of Bacillus subtilis. PLOS Genetics. 11. e1005046. (PubMed). (DOI: 10.1371/journal.pgen.1005046).

  • S. Durand, F. Braun, E. Lioliou, C. Romilly, A.C. Helfer, L. Kuhn, N. Quittot, P. Nicolas, P. Romby, and C. Condon (2015). A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis. PLOS Genetics. 11. e1004957 (PubMed). (DOI: 10.1371/journal.pgen.1004957).

  • C. Habib, A. Houel, A. Lunazzi, J.-F. Bernardet, A.-B. Olsen, H. Nilsen, A.E. Toranzo, N. Castro, P. Nicolas and E. Duchaud (2014). Multi-locus sequence analysis of the marine bacterial genus Tenacibaculum points to parallel evolution of fish pathogenicity and endemic colonization of aquaculture systems. Appl. Environ. Microbiol. 80. 5503-14. (PubMed). (DOI: 10.1128/AEM.01177-14).

  • H. Nilsen, K. Sundell, E. Duchaud, P. Nicolas, I. Dalsgaard, L. Madsen, A. Aspán, E. Jansson, D.J. Colquhoun, and T. Wiklund (2014) Multilocus sequence typing (MLST) identifies epidemic clones of Flavobacterium psychrophilum in Nordic countries. Appl. Environ. Microbiol. 80. 2728-36. (PubMed). (DOI: 10.1128/AEM.04233-13).

  • R. Avendaño-Herrera, A. Houel, R. Irgang, J.-F. Bernardet, M. Godoy, P. Nicolas, and E. Duchaud (2014) Introduction, expansion and coexistence of epidemic Flavobacterium psychrophilum lineages in Chilean fish farms. Veterinary Microbiology. 170. 298-306. (PubMed). (DOI: 10.1016/j.vetmic.2014.02.009).

  • B. Mirauta, P. Nicolas, and H. Richard (2014) Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models. Bioinformatics. 30. 1409-16. (PubMed). (DOI: 10.1093/bioinformatics/btu042).

  • G. Huet des Aunay, H. Slabbekoorn, L. Nagle, F. Passas, P. Nicolas, T.I. Draganoiu (2014) Urban noise undermines female sexual preferences for low-frequency songs in domestic canaries. Animal Behaviour. 87. 67-75. (DOI: 10.1016/j.anbehav.2013.10.010).

  • N. Strepparava, P. Nicolas, T. Wahli, H. Segner and O. Petrini (2013) Molecular epidemiology of Flavobacterium psychrophilum from Swiss fish farms. Dis Aquat Organ. 105 203-210. (PubMed). (DOI: 10.3354/dao02609).

  • E. Fujiwara-Nagata, C. Chantry-Darmon, J.-F. Bernardet, M. Eguchi, E. Duchaud and P. Nicolas (2013) Population structure of the fish pathogen Flavobacterium psychrophilum at whole-country and model river levels in Japan. Veterinary Research 44. e34. (PubMed). (DOI: 10.1186/1297-9716-44-34).

  • S. Laalami, P. Bessières, A. Rocca, L. Zig, P. Nicolas and H. Putzer (2013) Bacillus subtilis RNase Y Activity In Vivo Analysed by Tiling Microarrays. PLoS One. 8. e54062. (PubMed). (DOI: 10.1371/journal.pone.0054062).

  • J.C. Zweers, P. Nicolas, T. Wiegert, J.M. van Dijl, and E.L. Denham (2012) Definition of the Sigma-W Regulon of Bacillus subtilis in the Absence of Stress. PLoS One. 7. e48471. (PubMed). (DOI: 10.1371/journal.pone.0048471).

  • T. Rochat, P. Nicolas, O. Delumeau, A. Rabatinová, J. Korelusová, A. Leduc, P. Bessières, E. Dervyn, L. Kràsny, and P. Noirot. (2012) Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis. Nucleic Acids Res. 40. 9571-83. (PubMed). (DOI: 10.1093/nar/gks755).

  • A. Delauné, S. Dubrac, C. Blanchet, O. Poupel, U. Mäder, A. Hiron, A. Leduc, C. Fitting, P. Nicolas, J.-M. Cavaillon, M. Adib-Conquy, and T. Msadek. (2012) The WalKR System Controls Major Staphylococcal Virulence Genes and Is Involved in Triggering the Host Inflammatory Response. Infect. Immun. 80. 3438-53.(PubMed). (DOI: 10.1128/IAI.00195-12).

  • S. Durand, L. Gilet, P. Bessières, P. Nicolas, and C. Condon. (2012) Three Essential Ribonucleases-RNase Y, J1, and III-Control the Abundance of a Majority of Bacillus subtilis mRNAs. PLoS Genetics. 8. e1002520 (PubMed). (DOI: 10.1371/journal.pgen.1002520).

  • P. Nicolas, U. Mäder, E. Dervyn, T. Rochat, A. Leduc, N. Pigeonneau, E. Bidnenko, E. Marchadier, M. Hoebeke, (41 authors), and P. Noirot. (2012) Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis. Science. 335. 1099-1103 (PubMed). (DOI: 10.1126/science.1206848).

  • J. M. Buescher, W. Liebermeister, M. Jules, M. Uhr, J. Muntel, (43 authors including P. Nicolas), J. Stelling, S. Aymerich, and U. Sauer. (2012) Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism. Science. 335. 1099-1103 (PubMed). (DOI: 10.1126/science.1206871).

  • C. Ambroset, M. Petit, C. Brion, I. Sanchez, P. Delobel, C. Guérin, H. Chiapello, P. Nicolas, F. Bigey, S. Dequin, and B. Blondin. (2011) Deciphering the Molecular Basis of Wine Yeast Fermentation Traits Using a Combined Genetic and Genomic Approach. G3. 1. 263-281 (PubMed). (DOI: 10.1534/g3.111.000422).

  • M. Escobar, P. Nicolas, F. Sangar, S. Laurent-Chabalier, P. Clair, D. Joubert, P. Jay, and C. Legraverend. (2011) Intestinal epithelial stem cells do not protect their genome by asymmetric chromosome segregation. Nature Communications. 2. e258. (PubMed). (DOI: 10.1038/ncomms1260).

  • B. Fleuchot, C. Gitton, A. Guillot, J. Vidic, P. Nicolas, C. Besset, L. Fontaine, P. Hols, N. Leblond-Bourget, V. Monnet and R. Gardan. (2011) Rgg proteins associated with internalized small hydrophobic peptides: a new quorum-sensing mechanism in streptococci. Mol. Microbiology. 80. 1102-1119 (PubMed). (DOI: 10.1111/j.1365-2958.2011.07633.x).

  • M. Dalmasso, P. Nicolas, H. Falentin, F. Valence, J. Tanskanen, H. Jatila, T. Salusjärvi, and A. Thierry. (2011) Multilocus sequence typing of Propionibacterium freudenreichii. Int. J. Food Microbiol. 145. 113-120 (PubMed). (DOI: 10.1016/j.ijfoodmicro.2010.11.037).

  • U. Mäder, P. Nicolas, H. Richard, P. Bessières and S. Aymerich. (2011) Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Current Opinion in Biotechnology. 22. 32-41(PubMed). (DOI: 10.1016/j.copbio.2010.10.003).

  • P. Nicolas, A. Leduc, S. Robin, S. Rasmussen, H. Jarmer and P. Bessières. (2009) Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics. 25. 2341-2347 (PubMed). (DOI: 10.1093/bioinformatics/btp395). Program and data available here.

  • A. Barinov, V. Loux, A. Hammani, P. Nicolas, P. Langella, SD Ehrlich, E. Maguin and M. van de Guchte. (2009) Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram positive bacteria. Proteomics. 9. 61-73. (PubMed). (DOI: 10.1002/pmic.200800195).

  • P. Nicolas, S. Mondot, G. Achaz, C. Bouchenot, J.-F. Bernardet and E. Duchaud. (2008) Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Appl. Environ. Microbiol. 74. 3702-9 (PubMed). (DOI: 10.1128/AEM.00244-08). A new version of the Flavobacterium psychrophilum MLST database can be accessed here.

  • M. Ibrahim, P. Nicolas, P. Bessières, A. Bolotin, V. Monnet and R. Gardan. (2007) A genome-wide survey of short coding sequences in streptococci. Microbiology. 153.3631-44. (PubMed). (DOI: 10.1099/mic.0.2007/006205-0).

  • P. Nicolas, P. Bessières, SD Ehrlich, E. Maguin and M. van de Guchte. (2007) Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract. BMC Evol Biol. 7. 141 (PubMed). (DOI: 10.1186/1471-2148-7-141).

  • E. Duchaud, M. Boussaha, V. Loux, J.-F. Bernardet, C. Michel, B. Kerouault, S. Mondot, P. Nicolas, R. Bossy, C. Caron, P. Bessiéres, J.-F. Gibrat, S. Claverol, F. Dumetz, M. Le Hénaff and A. Benmansour. (2007) Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nature Biotechnology. 25. 763-9. (PubMed) (DOI: 10.1038/nbt1313).

  • P. Nicolas, K.M. Kim, D. Shibata and S. Tavaré (2007) The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns. PLoS Computational Biology. 3. e28.(PubMed). (DOI: 10.1371/journal.pcbi.0030028).

  • K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin, M. Hoebeke, P. Bessières and J-F. Gibrat. (2006) AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res. 34. 3533--3545. (PubMed). (DOI: 10.1093/nar/gkl471).

  • P. Nicolas, F. Sun and L.M. Li. (2006) A model-based approach to selection of tag SNPs. BMC Bioinformatics. 7. 303. (PubMed). (DOI: 10.1186/1471-2105-7-303).

  • M. van de Guchte, S. Penaud, C. Grimaldi, V. Barbe, K. Bryson, P. Nicolas, C. Robert, S. Oztas, S. Mangenot, A. Couloux, V. Loux, R. Dervyn, R. Bossy, A. Bolotin, J.M. Batto, T. Walunas, J.-F. Gibrat, P. Bessières, J. Weissenbach, S.D. Ehrlich and E. Maguin. (2006). The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci USA. 103. 9274-9. (PubMed). (DOI: 10.1073/pnas.0603024103).

  • P. Nicolas, A.-S. Tocquet, V. Miele, F. Muri (2006) A reversible jump Markov chain Monte Carlo algorithm for bacterial promoter motifs discovery. J Comput Biol. 13. 651-67. (PubMed). (DOI: 10.1089/cmb.2006.13.651).

  • A. Marin, T.E. Malliavin, P. Nicolas, M.A. Delsuc (2004) From NMR chemical shifts to amino acid types: investigation of the predictive power carried by nuclei. J Biomol NMR. 30.47-60. (PubMed). (DOI: 10.1023/B:JNMR.0000042948.12381.88).

  • C. Robert, M.-O. Bancal, P. Nicolas, C. Lannou, B. Ney (2004) Analysis and modelling of effects of leaf rust and Septoria tritici blotch on wheat growth. J Exp Bot. 55. 1079-94. (PubMed). (DOI: 10.1093/jxb/erh108).

  • M. Hoebeke, P. Nicolas, P. Bessières (2003) MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics. 19. 859-64. (PubMed). (DOI: 10.1093/bioinformatics/btg101).

  • K. Marrocco, A. Lecureuil, P. Nicolas, P. Guerche (2003) The Arabidopsis SKP1-like genes present a spectrum of expression profiles. Plant Mol Biol. 52. 715-27. (PubMed). (DOI: 10.1023/A:1025056008926).

  • P. Nicolas, L. Bize, F. Muri, M. Hoebeke, F. Rodolphe, S.D. Ehrlich, B. Prum, P. Bessières (2002) Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res. 30. 1418-26. (PubMed). (DOI: 10.1093/nar/30.6.1418).